Need help. I have a 87 MJ with 4.0 and auto transmission that I bought a couple months ago. The trans shifted fine with no problems untill I replaced the rear main seal on the motor. Finished up the seal early sunday and drove the truck around the rest of the day as usual with no problems. Went to go to work the next morning and the trans wouldn't shift out of second and had to use my other truck. Got home that evening and test drove it and it shifted fine. The next morning same problem and wouldn't shift. So far I have changed the fluid and filter (fluid was dark brown) and replaced a section of line that was mashed flat and I also looked to see if I accidently damaged any elect lines when I pulled the oilpan and found nothing. I don't know what else to do. The truck was unhooked from the battery for about two days when I replaced the seal so do you think it could have caused any computer problems?